The Australian Medical Association (AMA) has made formal notifications to the Northern Territory Government that federal immigration detention is harming children.

The AMA said their members were legally required to report damage being caused to children under the Territory's mandatory child abuse reporting legislation.

Dr Peter Morris from the AMA NT said two detainees who attempted suicide at the Wickham Point detention centre were among the steady stream of traumatised asylum seekers who have been brought through the doors of Royal Darwin Hospital.

"Unfortunately the situation's not getting any better and we're particularly concerned about the very negative impact on children," he said.

Church leaders have described the Federal Government's treatment of unaccompanied children seeking asylum as "state-sanctioned child abuse".

In a report titled Protecting The Lonely Children, the Australian Churches Refugee Taskforce says the treatment of unaccompanied child asylum seekers is a "sick joke".

Immigration Minister Scott Morrison has flatly rejected the claims, but the taskforce is calling for him to be stripped of his guardianship role of children in immigration detention.

"Children in our detention facilities are suffering everything from untreated sexual infections to tuberculosis ... they're biting themselves, they're banging their heads into furniture due to their appalling state of mental health."

Immigration Minister Scott Morrison has confirmed several asylum seekers were injured when staff shut down a week-long protest at the Christmas Island detention centre yesterday.

The ABC understands around 70 male detainees, who had been protesting to mark 100 days since the death of Iranian asylum seeker Reza Berati on Manus Island, were removed by specially trained staff and taken to a high-security facility known as 'Red Block'.

Mr Morrison has told Parliament some detainees became aggressive and had to be restrained after detention centre operator Serco called in an emergency response team.

He says four people were "taken to hospital for a range of injuries including suspected sprains or broken bones".

Doctors treating asylum seekers on Christmas Island have detailed disturbing allegations that some detainees are suffering life-threatening medical conditions as a result of detention, and children are showing serious developmental and mental health problems.